Schwazer, who was one of Italy's big medal hopes, was excluded from last year's London Olympics after testing positive for the banned blood-boosting substance EPO days before the start of the Games. He was banned for three-and-a-half years by Italian authorities earlier this year.
"The IAAF is aware of and shocked by the accusations made against it in (the) New York Times concerning the ongoing investigation in Italy regarding the case of the sanctioned Italian race walker Alex Schwazer," the body said in response to an article published on Tuesday.
The newspaper said that the IAAF had evidence of Schwazer using banned substances but did nothing to stop him from going to London until a test conducted by the World Anti-Doping Agency (WADA) turned out positive.
"The IAAF categorically refutes these claims in the strongest possible terms. The case outlined involved abnormal blood results with respect to an Athlete's Biological Passport and was handled in strict accordance with IAAF rules and those of WADA," the association said in a statement.
"As the investigation is ongoing, the IAAF will make no further comment at this time," it said.
The New York Times said the suggestion of the IAAF's prior knowledge of the athlete's use of banned substances had come from the Italian prosecutors' investigation.
Schwazer became a hero in Italy at the Beijing 2008 Games when he won gold by knocking more than a minute off a 20-year-old Olympic record set by Vyacheslav Ivanenko of the former Soviet Union, despite challenging conditions.
A tearful Schwazer admitted to doping days after the positive test was confirmed last year, saying he was relieved that his secret had been revealed.
Schwazer suggested he had actually wanted to get caught because the guilt was psychologically devastating. He said he could have tried to skip the July 30 doping test knowing he had done a final injection the previous day, but did not.